The End is Nigh
by Reefgirl
Summary: When Jack returns after the year that never was he doesn't get the warm welcome he was expecting, instead he finds the team breaking up. Crossover with SG1 and Stargate Atlantis. Epilogue: In which Jack says goodbye to the team and goes back to the stars
1. Homecoming

Rating: T for language

Spoilers: Everything including the last 3 eps of the last series of Dr Who

Pairings: Many and varied

Summary: When Jack returns to the Hub after The Year That Never Was he finds a less than warm welcome and the team breaking up. Crossover with SG-1 and Stargate Atlantis

Disclaimer: Don't own any of it. I do own Delilah she's an OC from my Atlantis fics

Authors Notes: Bit of an angsty one from me this time as the bunny just wouldn't give up. He fancied seeing what would happen if things weren't all moonlight and roses when Jack got back.

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Jack strode across the plaza and jumped on the kerbstone lift, he couldn't wait to see his team again, the memory of them and the things they'd done had kept him going through the months of torture at the hands of the Master. Owen, Gwen and Tosh looked around at the sound of the lift and saw the bottom of a long blue coat come into view, Gwen gave a squeal, leapt off her chair, ran towards the lift and threw herself into his arms

"Oh thank God you're ok, what the hell happened to you, where have you been?" she said. Jack laughed

"All in good time" he said

"I'll go and get some coffee and then you can explain everything" replied Gwen as Jack walked towards the others. He looked at their faces and saw they were not so pleased to see him

"Owen" said Jack as he stuck out his hand, Owen defiantly shoved his hands in his pockets

"S'pose you'll be wanting your desk back?" he said as he pushed past him and began to clear his stuff off Jack's desk. Jack held his arms out to Tosh

"Tosh" he said, expecting her to give him a hug, instead she slapped him hard across the face

"Bastard, you abandon us and run off with the Doctor, no reason, no explanation, nothing, we spend months searching for you and then you stroll in here like nothing's happened and expect us to be pleased to see you" she spat. Jack recoiled from the fury on her face as Gwen appeared with three cups of coffee

"Tosh please, let him explain first" she said, Jack looked at the floor

"I can't, not yet I need time, I will tell you I promise but not yet" he said. Tosh snorted in disgust

"Typical Jack Harkness, fine keep your bloody secrets see if I care, Ianto was right you _are_ a monster" she said, Jack looked around, for the one person missing from this gathering

"Where is Ianto?" he asked. Gwen, Owen and Tosh all looked at each other

"Gone" said Owen

"Gone? What do you mean gone" retorted Jack

"He left three months ago, he went to America with his neighbour Delilah, he works for Stargate Command now" replied Tosh with smug satisfaction. The colour drained from Jack's face, the one person he desperately wanted to see had gone

"Why?" he asked in a whisper

"Why do you think? You left him and ran off with the Doctor" said Tosh

"Tosh" said Gwen, a warning tone creeping into her voice but Tosh was on a roll.

"No Gwen, I'm not going to mollycoddle him, he's going to hear this like it or not, Ianto loved you and you just messed with him, teased him, used him and when you got tired of him you moved on to someone else, the Doctor of all people. He was there when Torchwood One was destroyed, when Lisa was being turned into a Cyberman and he blamed the Doctor for all of that, for God's sake that's why Torchwood was created in the first place, to track the Doctor down and you run off with him, you betrayed Ianto and I will _never_ forgive you for that" she yelled. Tosh sat down with her back to him so he couldn't see the tears running down her face, Owen put his hand on her shoulder and took up the tirade

"He was really cut up when you left but when he saw you on the news, running around London with the Doctor and the coloured bird and Harold Saxon saying that you were all 'Britain's Most Wanted', that's when he really flipped" he said

"Flipped?" Jack said fearfully

"Yeah, he went totally tonto when he saw that news report and smashed the place up, it took all three of us to hold him down" Owen replied. Jack put his head in his hands

"Oh my God, I had no idea" he said

"Bet you never gave us a second thought, didya?" Owen sneered

"Owen" pleaded Gwen

"Anyway, we asked Delilah to look after him while Harold bloody Saxon sent us off to the Himalayas, he came back to work then three months ago he told us him and Delilah were off to the States, the end" he said

"Why didn't you stop him, retcon him or something?" ask Jack

"Because he deserves better that's why" snapped Tosh. Owen patted her on the shoulder

"C'mon lets go and 'celebrate' " he emphasised the celebrate "our leaders return in the pub" he said, Tosh wiped her eyes and grabbed her coat

"Coming Gwen?" she asked. Gwen looked from them to Jack, who was now slumped on his desk with his head in his arms

"I'll join you later" she said as she gently squeezed Jack's shoulder, letting him know she was still there for him.


	2. Learning the Truth

Disclaimers: Same as Chapter 1

Authors Notes: Thanks for the reviews and alerts, if you're going to put me or your alert list please leave a review too, I'd like to know what you all think.

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**Meanwhile in the pub...**

Owen put a glass of wine on the table in front of Tosh and sat down

"That went well didn't it" she said with a wry smile, Owen took a mouthful of his beer

"He deserved every word" he chuckled "never thought I'd catch myself defending the Tea Boy in front of Jack" he looked at Tosh, allsorts on emotions were flickering over her face "c'mon, spit it out before it chokes you" he said.

"You remember Colonel Sam Carter from the SGC?" she said, Owen nodded

"Yeah, she asked for your help with some 'harmless'" he made air quotes "piece of space junk that turned out to be some kind of interplanetary time bomb". Tosh nodded "that could have wiped out half the solar system" she nodded again "and you saved the day, again," he said as she blushed

"Yes" she leaned forward to whisper "well I got an email from her a few weeks back, she's now in charge of their Atlantis project and asked me to join the expedition". Tosh's face lit up "Atlantis is a city in the middle of the ocean on a planet in another galaxy, can you imagine that, I'll be up to my knees in alien tech it's everything I've ever dreamed of" she said

"But?" replied Owen.

"I stalled her at first because I didn't want to leave you and Gwen in the lurch but now Jack's back...I want to get out, I need to get out before I end up like Suzie" she said. Owen gave her hand a squeeze

"Go, it's a once in a lifetime shot, don't worry about me and Gwen" he replied

"Come with me, with all your knowledge on alien biology they'd snap you up" she said. Owen snorted

"With my reputation! They'll leave me on some deserted planet within a week" he retorted

"You've cleaned your act up a lot since you took over" Tosh replied, Owen smiled.

"Thanks, but I'll never be Torchwood's golden boy, I have been thinking about moving on though" he said

"Really" replied Tosh in surprise

"Yeah, I've been chatting to Jim at Torchwood Two and he's leaving in a couple of months so I thought I might take over, ask Gwen to come with me and make a fresh start. I don't want to get out altogether but if we get away from the rift we might not end up going the way Suzie did" he said, Tosh smiled sadly

"I never wanted to admit it but perhaps Ianto's leaving was the best thing that happened to us, I'd never have had the nerve to even consider going until he left" she said. Owen tapped his glass against hers

"Here's to the tea boy" he said with a grin.

**Back at the Hub...**

Gwen tapped gently on the conference room door trying not to notice her boss had been crying

"Come on in Gwen" Jack said with forced cheerfulness. Gwen entered and placed another cup of coffee in front of him

"You'll have to forgive Tosh, she took your disappearance and what happened to Ianto very hard" she said apologetically

"I guess I deserved it, when I heard the Tardis engines I just took off, I needed my answers but I never gave what the consequences would be a second thought" he replied.

"Maybe if you explained" she said, Jack shook his head

"I can't I really can't, not at the moment, when I can actually put it into words I will I promise" Gwen nodded and sat down "what really happened to Ianto?" he asked, she sighed.

"Pretty much what Tosh and Owen said really" she replied

"Tell me please" he asked.

"Well, first of all we thought you'd gone off in a sulk after the business with Abaddon and opening the rift and you'd be back in a couple of days, after that we started to get really worried, we'd be out everyday searching for you then we found the city's CCTV footage of you running towards an old fashioned police box, Ianto identified it as the Doctor's ship, the Tardis and that's when he slid into a depression". Jack put his head in his hands

"I knew he was there at Canary Wharf and I knew he knew about the Doctor's involvement in all that but I had no idea how much it had affected him I just thought he was angry over what happened to Lisa" he replied.

"None of us knew how much it had affected him, not until that day we saw you on the news, Ianto had been getting worse over the week, his mood swings were beginning to affect his judgement, even Owen was becoming worried he wanted to send him for psychiatric help. Just after the election we saw that news footage of you and the Doctor running around London and Harold Saxon was saying you were terrorists and some such rot, well Ianto got really quiet it was eerie, like the calm before the storm and that really worried us, Owen wanted to force him to get some help, he could see he was about to snap. We knew something was going seriously wrong when Myfanwy flew up from the vaults in such a state, she was scared, I know it sounds funny now but she was terrified she hid under my desk and refused to come out, so we went downstairs and found Ianto smashing the place up "Gwen shivered at the memories of that day "it took us an hour to get him under control and sedated it was terrible" she subconsciously massaged the ribs that had been broken during the incident."Anyway we finally got him down to the med bay and agreed to take turns to watch over him, Owen didn't want him to be left alone but then we got a call from Harold Saxon to go to the Himalayas, we didn't want to go but in the end we had no choice so we called on Delilah, his neighbour. We'd met her a couple of times and Ianto told us he'd found out she used to work for Stargate Command, he said he'd become suspicious that something was not quite right when she started getting a lot of visits from the American military, Owen thought she'd been sent to spy on us but Ianto said it was rubbish but it turned out she did know about us, she'd done the same as Ianto and checked up on us. So we thought she'd be the best person to look after him, seeing as she was in the trade so to speak we could rely on her to keep quiet in case he rambled, after we got back from the trip to the Himalayas he was pretty much back to his normal self, better in fact but then. I don't know, he got itchy feet I suppose and hit us with the news Stargate Command had offered Delilah her old job back and offered him one too, on her recommendation, so they left, he's happy in his job and talks a lot about their friends" said Gwen.

"Did you try and talk him out of it?" asked Jack, Gwen thought carefully, they'd made the obligatory 'Don't go' noises but deep down they'd all agreed that Ianto deserved every chance of happiness and had let him go with all his memories intact

"There was no point, he was determined to go" she replied. Jack started tapping his fingers on the table as he was thinking

"Have you got a number for him" he asked, Gwen nodded

"I don't know if either of them will be pleased to hear from you, Delilah heard all about you and, well , she's not exactly your biggest fan now" she replied

"I don't care call him" demanded Jack. Gwen sighed and dialled, Jack leaned over and put the phone on speaker

"Hello" a voice singsonged over the phone

"Hi Delilah, is Ianto there" said Gwen

"Hold on a moment, Maria what _are_ you doing? I've just packed that box...well what's Bagpuss doing in there in the first place?...playing hide and seek with the mice, serves me right for asking...ok just put everything back neatly, sorry Gwen you were saying" said Delilah with a chuckle

"Is Ianto there?" repeated Gwen.

"No he's...um...away from the base for a couple of days, do you want me to give him a message?" Delilah replied

"Um...just tell him Jack's back" said Gwen

"Is he" Delilah paused "don't think that's a good idea do you" she said

"Why the hell not?" retorted Jack

"Captain Harkness I presume?" Delilah said, her voice turning cold.

"And you're Delilah" he replied

"That's Dr Stirling to you Captain" she said

And I say again why not?" he snapped.

"Because Ianto's finally got his life back in order, he's happy and the people here care for him, I _will not_ let anyone destroy that, especially you, I don't want him to go through all that again because of your ego" she hissed.

"Delilah please" Gwen's voice took on a pleading tone "let Ianto decided, you can't protect him forever" she said, Delilah sighed

"I'll let him know you called, will that do you" she replied.

"Thanks" said Gwen

"Now, if you'll excuse me I have to rescue a saggy old cloth cat from a box of books" Delilah said with a chuckle "bye"

"Bye" said Gwen and hung up

"Who the hell does she think she is?" shouted Jack.

"She's someone who saw Ianto go through hell and helped him come out the other side with his sanity intact, that's who" snapped Gwen. Jack ran his hands through his hair

"I'm sorry, I shouldn't have said that, she obviously cares a lot for him" he replied

"S'ok" said Gwen slightly mollified now "now what"

"I'm going to Stargate Command that's what, I've got enough contacts to bypass the red tape and get in and I'm coming back with Ianto, trust me" Jack said as he swept past Gwen and ran down the stairs towards his quarters

"Jack...Jack" he disappeared down the manhole cover "I don't think he wants to come back" said Gwen with a sigh.


	3. Communication Problems

Disclaimers: Same as Ch1

Spoilers: Mainly from Stargate SG-1

AN: Thanks again to all the readers, I'm hoping to update daily, maybe twice I don't know

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**At Stargate Command...**

The lift door opened and Jack saw the man he was supposed to meeting, General Hank Landry

"Captain Harkness?" he said, Jack smiled and shook his hand

"Thanks for arranging this for me" he replied. The General laughed

"If you want your man back you're going to have quite a fight on your hands, I've already got the chief engineer on the Daedalus, our own Dr Lee and Colonel Carter on Atlantis demanding he work for them" he replied. Jack frowned; it looked like it wasn't going to be so easy to get Ianto back

"Let's hope they won't be too disappointed when he decides to come home" Jack replied. Landry led him through the Gateroom and into his office

"I've arranged for you to talk to him via a link to the Daedalus, where he's stationed at the moment, Walter!!" he yelled for his Chief

"Dr Novak is online and waiting for you on your terminal sir" called back Sgt Walter Harriman. Landry sighed and rolled his eyes

"I swear he gets more like Radar every day" he said, he sat in front of his computer and greeted the thin faced woman with her hair tightly pinned in a bun, Jack thought she looked terrified of the General

"General Landry...um...what...um...is...is...'hic' oh damn" she took a deep breath and tried to calm herself "is there a problem 'hic' oh for God's sake" she said. Landry chuckled

"She gets hiccups when she's nervous" he murmured to Jack

"So I see" he whispered back

"No Dr Novak there's no problem, I've got someone here who wants to speak to your Mr Jones" he said as he got up and Jack sat in his place, he flashed his megawatt grin at her causing her to fumble and drop her pen

"Hi, can I speak to Ianto please" he said

"Sure" she dropped her pen again "I...um...I'll just give him 'hic' oh kill me now, Ianto!!'Hic' you're 'hic' wanted" she called. She got up and left the chair empty for Ianto, Jack could hear his voice coming nearer

"Lin, stand on your head and drink a glass of water" he yelled, then ducked as a pen flew in his direction, he sat down chuckling and looked up at the screen, his face instantly slipped into the bland mask that Jack knew so well

"What can I do for you sir?" he asked formally. Of all the scenarios Jack had imagined their reunion to be, this definitely wasn't one of them, all smart remarks, innuendos and double entendre's that he's planned to use fled from his mind

"I want you to come back to Torchwood" he said simply, Ianto gave a bitter laugh

"Why?" he asked. At the back of his mind Jack had expected Ianto to come running when asked to return, put on the back foot he fumbled for an answer

"Um...we need you back at Torchwood, we miss you" he said lamely

"Right, you need me, in other words you can't work the coffee machine" Ianto sneered

"No, it's not like that, we were a team Yan" said Jack.

"A team!" Ianto was incredulous "A team, you Tosh, Owen, Suzie and then Gwen were a team, I was the one who cleared up after you, the one who made sure Torchwood's tracks were covered, the one who was left behind when you all went out to celebrate saving he world, the one who was only missed when the coffee was late and the only one who ever made the bloody coffee, that's how much of a 'team' we were Jack". Jack flinched as all Ianto's hurt and anger came spilling out "the one time I really thought you cared, the one time I thought I could let you in without having my heart trampled on you ran off and left with the Doctor, oh I know all that nonsense about having to 'find your answers' but you wouldn't even tell me what the questions were, that's how much you trusted me" he said.

"Ianto please, let me explain" Jack begged

"Which basically means you'll lie your head off" retorted Ianto

"No, I promise, just come back to Torchwood and I'll explain everything, the whole truth about me, the Doctor, my past and what happened when I left, please Yan, please come back, I need you" Jack pleaded.

"No, I'm not coming back to Torchwood, I've got a job I love, one where I can actually use the skills I was trained for, I've got a group of friends that I care for and who care for me in return and I've got respect, something I _never _got from you, why would I throw all this away to become your whipping boy again?" he spat. Ianto's resolve nearly cracked when he saw the look of devastation on Jack's face, but he couldn't give in, if he cracked now he may as well get his suits out of storage,

"Put like that I can see why you don't want to leave" said Jack softly

"I'm..." Ianto pulled himself up sharply, why should he be sorry "I'm going to have to go Jack I've got work to do, give my love to Tosh, Owen and Gwen" he said as he got up and left. Jack slumped forward and slid his hands into his hair, how had it all gone so horribly wrong, his ego said that Ianto was wrong and he'd never meant to do any of those things and Ianto had read him all wrong, but the rest of him admitted that every word Ianto had spoken was true, just as Tosh's had been the day he returned to the hub, he was a monster who had no regard for anyone but himself, no matter how hard he pretended that he'd changed, underneath he was still that reckless playboy who was out for what he could get and didn't care who he hurt in the process. He looked up as Dr Novak cleared her throat

"Um...do you want me to get him to call you back when he's calmed down a bit?" she asked, Jack shook his head

"No, I'll try later, face to face, if he'll see me" he replied, she smiled

"If you're sure" she said, Jack nodded again and switched the monitor off.

* * *

Ianto slumped in his chair, he hadn't meant to say all of those things to Jack, not in quite that way but seeing his face again had bought all the pain to the surface, he had known Jack was back, Delilah had told him Gwen had called with the news that he'd returned, he wasn't going to call back but Delilah had told Gwen she'd get him to call so he did, only to be told Jack was on his way to Colorado to bring him back, his resolve had hardened, he wasn't going to be dragged back to Wales like some naughty schoolboy so he'd volunteered to go aboard the Daedalus to help with their battle simulation programme. He took a gulp of coffee, which reminded him even more of his old life and threw the mug against the bulkhead,

"Why don't you take a break, Dr Zelenka can take over for a while if you want" said Dr Lindsey Novak as she gently squeezed his shoulder

"Yeah maybe I should, before I do more damage to the mug stocks" he replied with a wry smile

"I think he's going to try again, when you get back to Earth I mean, he said he was going to try face to face" she said

"It won't work, I'm not going to leave the SGC, I'm not going to let him walk all over me, not again" he retorted

"At least talk to him, now all the yelling and screaming is out of the way you might be able to be reasonable with each other" she said. Ianto thought it over

"Maybe, I'll see how I feel later, do you fancy some tea?" he said with a grin, Lindsey laughed

"Yeah, why not, now that coffee's off the menu" she replied.

**Back at Stargate Command...**

Jack got out of the chair and headed for the Gateroom where Landry and his Sergeant was going over some computer logs

"Thanks for letting me use your office, you're right I am going to have a fight on my hands getting him back" said Jack. Landry and Walter looked at each other, the couldn't help overhearing some of the heated exchange between the Torchwood head and his former employee,

"If you don't have to hurry off I can arrange for you to join one of my teams who are going aboard the Daedalus to observe tomorrow's battle simulation" Landry said. Jack smiled

"Thanks, I'd like that" he replied

"It'll give you a chance to sort out your problems" Landry said with a look that said I know just what you're going through.

**The Next Day...**

At 08.00 Jack joined SG-1 as they waited for the Gate dialling sequence to begin. Jack had spent the evening with the team he'd be observing the war games with and had found them to be extremely pleasant company; Colonel Cameron Mitchell had reminded him of what he'd missed about the company of soldiers. Daniel Jackson reminded him a little of Tosh with his enthusiasm for his chosen subject and his ability to keep the peace within the team, Vala Mal Doran was a female version of himself and that scared him witless, her smile was the same, her attitude to life and her recklessness the same, even her flirting with Daniel and Cameron was the same as his. Teal'c was the one who intrigued him the most, the big alien had said little all night, he seemed happy to observe the proceedings, he had an air about him that Jack had seen on only one other being before, the Doctor, Teal'c was old, older than the rest of his team, maybe even as old as Jack and had seen a lot of the same things as he had, Jack could tell from his eyes.

Jack took a step back as the Stargate splashed open

"I can never get enough of that" said Colonel Mitchell as he stepped up onto the ramp "c'mon lets move out, we don't want to keep Colonel Caldwell waiting", Vala linked her arm through Jack's.

"It's a shame this planet is uninhabited, I wanted to take you to Cyranos, there's this little tavern in the village by the gate and they have this drink called Rycorn, and it's effects, well...hey, Daniel" she protested as Dr Jackson grabbed her arm, pulled her away from Jack and started whispering in her ear, Jack continued up the ramp with Teal'c so he missed the look on Vala's face as Daniel's words began to sink in. Vala's eyes widened as the penny dropped

"Oh, that explains everything, I wondered why I was getting nowhere" she folded her arms and sighed as she trudged up the ramp "what a waste" she said.


	4. Communication Restored

Disclaimers: Same as Ch1

AN: This is mainly Jack and Ianto but the majority of the background story is set after the end of the last series of SG-1.

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**On the Daedalus...**

Ianto was going through the Battle Simulation programme he had helped Dr Radek Zelenka create; with a little help from Tosh they had added a few surprises to the proceedings.

"I hear your old boss is joining SG-1 in the observations" said the heavily accented voice of Dr Zelenka, Ianto almost laughed out loud, he'd managed to keep Lisa a secret from Jack and the others for over a year but here on a Star ship with a crew of a couple of hundred, tales of his argument with Jack and rumours of whether their relationship was more than just boss man and disgruntled employee had begun to circulate in twenty minutes.

"So I heard" Ianto replied

"I take it you're not happy?" Zelenka remarked

"It's something I can do without" said Ianto

"He can't be as bad as Dr McKay" said Radek with a chuckle "no-one is".

"Egotistical, thinks he can do no wrong and you have to spend the majority of your time covering up his mistakes without so much as a thank you" replied Ianto bitterly

"To quote your friend Delilah, been there, seen it, done it" said Radek with a smile.

"So what's Dr McKay like?" asked Ianto

"Egotistical, thinks he can do no wrong, you have to spend the majority of your time covering up his mistakes etcetera" Radek replied with a chuckle. Ianto laughed out loud

"Does he try and get all his employees into bed?" Radek looked surprised and shook his head "lace every conversation with innuendo and double entendre's" he asked

"I do not think Rodney knows what a double entendre is" Radek said

"How about grabbing your arse every time you walk past him?" Ianto asked

"Definitely not" Radek said with a grin.

"Who's grabbing whose arse?" asked Dr Lindsey Novak

"Ianto's boss, the one who's coming here with SG-1 so you've got to, what is it Delilah says about Colonel Sheppard...Oh yes 'Break out the tin draws, the octopus is loose'" said Radek. Radek, Lindsey and Ianto were still laughing when Daniel Jackson appeared in the engine room with Jack

"And this is the engine room, this is Dr Novak she's the chief engineer and has the most experience of anyone on Earth with Hyperdrive engines, if you _really_ want to know how they work she'll tell you" said Daniel with a smile. Jack grinned and shook her hand

"Nice to meet you in the flesh and such sweet flesh too" he said, Lindsey blushed

"This is Dr Radek Zelenka, formerly of the Czech Republic but more recently the second in command to the scientific community on Atlantis, this is Captain Jack Harkness from the Torchwood Institute in the United Kingdom, you know Ianto of course" said Daniel.

"Ianto" said Jack, in greeting

"Jack" Ianto replied. Daniel handed Ianto a piece of paper

"I found this on a tablet a few weeks ago, it looks like an old Welsh dialect, I'm not asking for a translation but can you possibly give me an idea of what it says, when you've got time" he said

"I'll take a look later" Ianto replied. Daniel, Lindsey and Radek, sensing they were intruding, made excuses to be elsewhere

"Since when did Torchwood have an interest in battle simulations aboard a Spaceship?" Ianto asked

"Since yesterday" replied Jack, Ianto sighed

"There's nothing left to say, I'm not giving this up to go back to making coffee and clearing up your shit" he said.

"Tosh is leaving, you could have her job" said Jack, he knew he was clutching at straws, after having seen what Stargate Command was all about and been given a guided tour of the Daedalus, he wouldn't want to return either,

"So she's taken up Samantha Carter's offer, I wondered when she would" said Ianto, with the first genuine smile Jack had seen since he arrived.

"I take it that was your doing?" said Jack

"All I did was give her Tosh's name when she was having some problems with a piece of alien technology she found, the rest of it was her idea" replied Ianto, Jack sighed again, the team really was breaking up

"I'm sorry Yan, I really am, I never meant to hurt you but I _had_ to go, when I heard the Tardis engine's I had to take off, I knew he wouldn't hang around for long, I had just one shot at getting to him before he left, it's not like you can make an appointment with this doctor, I only just made it but I got my answers, I had to pay for them though. When it was all over the Doctor offered to take me with him again, I won't lie, I was sorely tempted but I wanted to get back to you all, you especially, I told Gwen I was going to bring you back and I wasn't taking no for an answer, but I can't do it, you'd hate me forever and I couldn't live with that so I'll just be happy knowing you've got what you've always wanted" said Jack with a sad smile. He held out his hand and Ianto shook it

"Thank you" said Ianto, glad that the ice was finally melting between them, he knew it would be a long, long time before he could forgive Jack for everything that had happened but the fact that he'd made an effort to track him down went a long way towards helping. Jack smiled in relief, thankful that things were thawing out between them, he couldn't kid himself that their relationship would ever be the same as it once was but at least they were talking and not shouting abuse at each other, perhaps this was the first tentative move in restoring their friendship.

Suddenly the ship shook under the force of an explosion, Ianto grabbed the console and Jack grabbed onto him as he lost his footing, sparks spluttered out of equipment and the lights flickered,

"What the hell was that?" said Jack. Lindsey Novak ran past

"The Orii have just exited hyperspace and opened fire" she said as she started to punch up figures on a screen "Hyperspace engines are offline, Sublight are at full power so are weapons and shields are down to eighty percent, but if we don't get the Hyperspace engines online we're sitting ducks"

"Do you need a hand?" asked Jack. Lindsey pulled a metal plate out of the floor

"Could you deal with the fried wiring down there?" she asked, Jack stripped off his coat and shirt

"Just like old times" he said with a grin as he disappeared down the hole.

"Dr Novak, report please" said the disembodied voice of the ship's commander, Colonel Steven Caldwell

"Hyperdrive's offline, sublight and weapons at full power, shields at eighty percent" she reported

"Do what you can Doctor, re-enforcements are coming but we're taking some damage, we'll need to jump into hyperspace to make repairs before long, hold on" they could hear muffled voices "SG-1 are on their way down, they have some information for you"

"Yes sir" replied Novak. Cameron, Daniel, Teal'c and Vala came running into the engineering deck

"Vala says the Orii have changed their shielding technology" said Mitchell

"Got a visit from Adria the other night, she hasn't changed much apart from becoming a Goddess to the believers, mother to a Goddess, who could have known" Vala smiled sadly "anyway she was boasting about great advances the Orii had made, she said that the new ships that had been built had used something like that phase shift thing that Sam built so they were there but not there, if you know what I mean" Vala laughed "she actually said the ships could carry more troops because they were bigger on the inside, like that's even possible" she said. Jack leapt out of the hole in the deck and ran over to the group, he was shaking

"What did you say? Did you say these Orii had ships that were bigger on the inside" he resisted the urge to shake Vala "tell me where you got this information from" he yelled, Vala was shaken by the look of horror on Jack's face.

"My daughter Adria, I was impregnated by the Orii a couple of years ago, they can't invade our galaxy themselves because they'd be defeated by the Ancients, they have some kind of Rule of the Ascended, Daniel knows more about it than I do, but to get around it they created Adria, she's an Orii in human form" Vala replied.

"The Ancients, the ones who built the gate system and Atlantis, learned to ascend to a higher plane of existence where they live as beings of energy, they watch over us but the don't get involved with us lesser beings, it's against the rules, some do break them but the penalties are stiff, some of them help us to find enlightenment so we can ascend at the point of death" Daniel smiled in embarrassment "done it twice myself" he explained.

"Adria died and ascended a year ago, she comes back sometimes to gloat, this time she told me how she'd tricked another race of beings that had ascended en mass after their world was destroyed into revealing some of their technology, she's good at that, from their knowledge she was able to instruct the priors on how to build new ships that could hold more troops but still appear the same on the outside" Vala said. Jack ran his hands through his hair and started to pace furiously

"Shit!! Fuck, fuck, fuck, I can't believe this is happening, it can't be happening, we are so screwed" he growled

"What's going on, what do you know?" said Mitchell. Ianto's face fell as it dawned on him what had happened

"Jack, is this what I think it is?" he asked, Jack nodded

"Your enemy has got its hands on Timelord technology" Jack said.


	5. Getting What You Want

Disclaimers: Same as Ch 1.

AN: The technobabble is just something I made up as I went along so there's no need to tell me it won't work.

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"That is not possible, the Timelords are a legend" replied Teal'c, Jack shook his head,

"They were destroyed in a time war, a couple did survive but now there's only one left" replied Jack,

"Hold on, are you saying that this race of...Timelords can really build ships that are bigger on the inside?" said Cameron Mitchell. Jack nodded,

"I used to travel with the last of the Timelords, the Doctor, I know a bit about their technology" he gave a smile "the amount of running repairs we had to do on the Tardis, it looks like they've managed to create the Time Vector Generator, a dimensional control unit". He looked at the blank faces of his companions "the inside of the ship occupies a different dimension to the outside" he replied,

"That is not possible" said Dr Radek Zelenka,

"Oh it's possible alright, just don't ask me how it works" Jack replied.

"Fascinating as this conversation is, how are we going to defeat the Orii and their super duper new bigger on the inside ships" snapped Mitchell,

"It all depends on what other technology they've got, the good news is they haven't created a Tardis, that's an organic creature and the Timelords were a peaceful race so I doubt weapons featured highly either, but you said that they had new shield technology, that could be a problem" Jack said,

"All Adria would tell me was that their new shielding was a combination of new technology and Sam's phase shifting, that's all I know" said Vala. Ianto pressed his earpiece,

"Colonel Caldwell, I need to send a data transmission back to Earth" he said,

"Is it urgent Mr Jones?" came the reply,

"Yes, I need an old colleague of mine to send me some information that could help us defeat the Orii sir" Ianto said,

"Ok, but make it short" Caldwell snapped,

"Yes sir" Ianto replied, he sat at his computer and quickly sent his transmission to the SGC with an instruction to pass it on to Torchwood in Cardiff.

"Care to tell us who you're emailing?" asked Mitchell,

"I took more than Lisa with me from Torchwood One, after the battle I took all the information we had on the Doctor and it was quite a lot" he said,

"Yeah, considering Torchwood's purpose that's not surprising" said Jack,

"But not all of the Doctor's companions were chance pick ups" said Ianto with a smirk,

"Are you telling me that Torchwood planted agents on the Tardis" replied Jack in disgust.

"There were projects going on that even Yvonne Hartman had no knowledge of, this was one of them, the less people who knew the better, I was one of only a handful who knew of this one" Ianto replied matter-of-factly,

"Some of the Doctor's companions were Torchwood agents?" Jack repeated,

"Yes, Liz Shaw, Jo Grant, Evelyn Smythe, Mickey Smith, to name a few" said Ianto.

"Mickey? Rose's Mickey was a Torchwood agent?" Jack retorted,

"We caught him trying to hack into our computer system, we bought him in and he told us about his girlfriend and the Doctor so we asked him to send us any information he could, we thought we'd struck gold when he started sending us all the technical details of the Doctor's Tardis" Ianto began.

"Not the idiot we thought he was" muttered Jack,

"After about a year the information dried up, we thought he'd got cold feet or a conscious or something so we retconned him and cut him lose" said Ianto coldly.

"I knew you Torchwood One types were heartless but this..." Jack began,

"But this is why we did what we did, so we could collect information to help us defend Earth, or had you forgotten that part of the Torchwood mandate, like you conveniently forgot about detaining the Doctor on sight" replied Ianto. Jack opened his mouth to defend himself,

"Hey!! Can we focus and leave your lovers tiff until _after _we've defeated the Orii" snapped Mitchell, Ianto ignored him,

"So I collated all the information we had at Torchwood One and bought it with me, when I left I gave the information to Tosh, she's the only one I could trust with it, I'm waiting for her to send it back to me via the SGC" he said. Jack opened his mouth to retaliate but the computer chirped, telling them Ianto had his reply, he turned to the screen and began to retrieve the data,

"Well?" asked Dr Lindsey Novak.

"If the Orii are using shields based on Tardis technology then we should be able to find weak point, we were able to get hold of the frequency that the Tardis shields operate on, thanks to Mickey" Ianto couldn't help himself, he had to get that dig in, "if we can get the weapons system on the same frequency then it would be just as if the shields weren't there" he said.

"What about the bigger-on-the-inside bit?" asked Mitchell,

"It's not a weapon as such, all that will accomplish is being able to carry more troops, if we can get around the shielding then it will have been a waste of time putting the Time Vector Generator in" said Jack.

"And the Phase Shift thing" said Vala,

"I will deal with that, I have done some work with Colonel Carter on this so I think I can find a way to make it ineffectual" said Radek,

"Ok get to work, I'll inform Colonel Caldwell on what we're doing" said Lindsey Novak, instantly taking charge.

**After a couple of hours...**

Lindsey Novak, with Jack's help, had managed to get the Hyperdrive engines working so they could jump and manage their repairs and modifications in relative peace, while Radek and Ianto had put together a programme that would allow the ships weapons to negate the new Orii/Timelord modifications to the ships.

When everything was ready, SG-1, Jack, Ianto and Radek took up positions on the Bridge,

"On station Sir" said Major Emma Cooper,

"Good, weapons?" replied Colonel Steven Caldwell, the Tactical Officer, Captain Josh Kleinman, tapped keys on his console,

"A one hundred percent and awaiting your orders Sir",

"Good, drop us out of Hyperspace Major" said Colonel Steven Caldwell. The Daedalus dropped into normal space and immediately came under fire from the Orii ships,

"Return fire, fire at will" barked Caldwell, Kleinman's fingers ran over his console,

"No effect Sir, shields down to eighty percent" he replied.

"Dr Zelenka, Mr Jones, what happened?" Caldwell asked,

"Checking now Colonel" replied Radek, he typed commands into the computer "we haven't got the right phase frequency, adjusting now", Ianto made a few more adjustments to the programme and nodded to Radek,

"That should do it" he said,

"Try now Colonel" Radek said. Caldwell nodded to Kleinman who fired, the nearest Orii ship glowed as the Daedalus' weapons struck, a cheer erupted from the Bridge,

"Keep firing, fire at will, fire at will" Caldwell ordered. The first ship exploded closely followed by another, the remaining Orii ships opened hyperspace windows and fled the battle. Ianto let out the breath he'd been holding, it had worked he couldn't believe it had worked, that mad idea he'd seen in Lisa's favourite episode of Star Trek had actually worked, he'd was brought out of his day dreaming by Radek clapping him on the shoulder,

"That was an inspired piece of work, wonderful, wonderful, how did you come up with it?" he said, Ianto blushed.

"I saw it on an episode of Star Trek, Lisa was a bit of a Trekkie on the quiet" he replied, Radek was just about to ask who Lisa was when Caldwell came over,

"Mr Jones, I'm impressed with your work, Dr Novak has asked that you be assigned to the Daedalus crew permanently and after what you did today I'm happy to endorse her recommendation" Caldwell shook Ianto's hand "welcome to the crew" he said, Ianto's brain finally caught up with events,

"Thank you Colonel Caldwell Sir, I'll be happy here, I know I will" Ianto replied as he accepted the congratulations of the crew. Jack's heart sank as he heard Ianto accept Caldwell's offer of a place on the crew of the ship, he knew Ianto would never return to Torchwood now, he'd clung to the vague hope that he'd be able to talk him into returning but now, he realised that nothing could stop his team breaking up. Earlier on he'd heard from Owen about taking over at Torchwood Two, he'd told him he'd think about it, really he was hoping that Ianto would come home and because of that Tosh would stay as well but it wasn't going to happen, not now, he may as well accept the fact that they were going to leave him.

**The Daedalus Mess Hall...**

Ianto was sitting alone nursing a cup of tea, over the last our he and Lindsey Novak had been celebrating his new job as a computer programmer, his first job would be make sense of all the stuff that had been left behind by Hermiod, their Asgard engineer. He was looking forward to burying himself in the Asgard's computer programmes, he was also looking forward to spending time in Atlantis, the Daedalus' primary job was ferrying supplies to the Pegasus Galaxy and at least he'd be able to see Radek and Tosh, if Jack let her go. He was so lost in his thoughts that he barely registered the man who sat himself in the chair opposite,

"I suppose congratulations are in order" said Jack, Ianto smiled at him,

"Thanks, I can't believe this is happening, it's like a dream" Ianto replied. Jack absent-mindedly ran his finger around the rim of his cup,

"The team is breaking up, you're here, Tosh is joining the Atlantis project, Owen and Gwen want to get away from the rift and start again at Torchwood Two in Scotland" he said,

"Oh, Jack I'm so sorry" Ianto replied, Jack smiled sadly.

"I'm not blaming you, I knew it would happen one day but not quiet so soon" he said,

"What about you, you could go to Scotland with Owen and Gwen" said Ianto, Jack shook his head,

"No, I can't do that they need to do their own thing, no I'm going to call a friend and go travelling, I've just made a decision, you are all doing what you've always wanted and so am I now" he said with his trademark grin.

"You're going back to the Doctor" Ianto smiled "you've always wanted to stay with him, your heart was never _really_ with Torchwood" Jack blushed, Ianto had always been perceptive where he was concerned "you only stayed because you knew the Doctor would have to come to Cardiff, so why did you come back to us?" he asked.

"Because I couldn't leave you, after all we'd been through I couldn't just leave, I foolishly thought we could carry on where we left off, I didn't realise the effect my leaving would have, especially on you, years ago I would have done anything to stay with the Doctor but when he offered to take me with him and Martha the first thing I thought was 'I can't leave the team' but I got back and found the team breaking up. I came here because I didn't want to lose you, any of you but now I can see I can't keep you forever, I've got to let you go" he said, Ianto rested his hand on Jack's,

"Thank you, for everything you did for me and thank you for letting me go to do this" Ianto replied.

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**AN: **This is the last 'Proper' chapter, there will be an epilogue to tidy things up.


	6. Epilogue: Letting Go

Disclaimer: Same as Ch 1

AN: Thanks to everyone who has read, reviewed and alerted this story, it's been fun to write

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**A few weeks later...**

Jack padlocked the front door of the little tourist office that was Torchwood Three's cover, it really was the end, he didn't doubt for a moment that the Torchwood Committee would let it lay idle, someone would take over in the future, build their own team, have their own adventures with the rift and the Weevils, but those adventures wouldn't include him. He'd returned to the hub without Ianto and told Tosh he'd given Samantha Carter a glowing reference, she could go with his blessing and take anything from the archives with her that would help the Atlantis Project, he then told Owen he'd do everything in his power to help in their take over of Torchwood Two. The rift between him and his team had mended after he'd told them about his leaving with the Doctor, truth about Harold Saxon and what had happened in The Year That Never Was, after that he'd thrown a leaving party that Cardiff would remember for years.

"Are you sure about this Jack?" asked the Doctor, Jack turned to his friend and smiled

"Yeah, I'm sure, we've been together for too long so I'll never be happy with another team, it's best to leave now and be happy knowing everyone is doing what they've wanted all along, including me" he replied with a grin. He picked up his bag and walked towards the Tardis,

"Ready?" the Doctor asked, Jack nodded, put his fingers to his mouth and whistled,

"You sure you don't mind me bringing her?" he said as Myfanwy swooped out of the sky and through the open door of the Tardis, both he and the Doctor winced at the yells and blue language coming from Donna,

"Not at all" the Doctor replied, Jack chuckled,

"It's good to be back" he said.

**A year after that...**

"How about a trip to Atlantis?" said the Doctor,

"Thanks, I'd like to see how Tosh and Ianto are doing" Jack replied. A couple of days ago they'd stopped off in Scotland to see Owen and Gwen, he'd been shocked by the change in both of them, they'd moved the offices of Torchwood Two out of Glasgow and into Torchwood House where they'd organised and archived all the files and artefacts that had been collecting dust over one hundred years, with help from one of Delilah's niece's who Ianto had sent to them saying she'd be an ideal Torchwood agent. The change in Owen had been incredible, he was no longer the hard drinking, womanizer he'd been in Cardiff, the way he'd thrown himself into the work of making Torchwood Two a success had made him almost unrecognisable, he'd become so dedicated to his work and the team he'd built from nothing that Jack couldn't help but feel proud of him, something he thought would never happen. Gwen had toughened up but not so much that she'd lost that spark of humanity that Jack had always admired, if anything it had grown, she was the mother hen of the group in Torchwood House, always there for anyone who needed her, Jack wondered that, maybe, if she'd joined his team earlier Suzie wouldn't have gone off the rails, Ianto may not have kept so much hurt bottled up and Tosh wouldn't have worked herself to a frazzle. He could see that Owen and Gwen's team were more like family to them than his team had been to him, they way Gwen chivvied them out of the door and sent them home in the evenings, they way she included everyone in the work, making sure no-one felt they were overlooked in anyway, when he left a couple of days later he knew Torchwood was in the right hands.

* * *

The Tardis had landed on the East Pier of Atlantis next to the Daedalus, Jack insisted that they go and present themselves to Colonel Samantha Carter, to avoid complications he'd said, the Doctor was all for just strolling in and damn the consequences until he'd come face to face with Major Lorne the head of security, 'ok maybe I should go and say hi to Colonel Carter' he'd said after arguing the toss with Major Lorne for ten minutes, which had ended in Lorne threatening to shoot him if he said another word. While Jack, the Doctor and Donna were with Colonel Carter Myfanwy had gone looking for food, following her nose she had found her way to the mess hall where she'd spotted Ianto, happy to see her friend again she launched herself at him with a screech, knocking him on his back in the process. Sam Carter had received a number of panicked calls from people in the mess hall saying that some kind of prehistoric bird was attacking one of the Daedalus crew, when Sam and the others arrived they found Myfanwy sitting on the back of Ianto's chair glaring at Major Lorne, Colonel Sheppard and their teams who were still pointing guns at her. Jack explained that Myfanwy wasn't dangerous just protective and the fact that she'd already given Dr's Radek Zelenka and Lindsey Novak a nasty nip was just her way of showing them who was number one in Tosh and Ianto's affections. The reunion had been a riotous affair even by Sheppard's standards, he'd learned that Tosh was something of a hero in the science department due to the way she took no crap from Dr Rodney McKay, Jack supposed it was due to the fact she'd worked with himself and Owen for so long that she could put up with anything. He understood from others that she'd become close to Dr Radek Zelenka and it made Jack incredibly happy, Tosh had never been sure of herself, sexually, and had used her work at Torchwood as an excuse to avoid relationships at all costs, they all had one way or another, seeing her so relaxed in the company of the scruffy Czech scientist made him glad she'd done the right thing by leaving Torchwood and joining the Atlantis Project.

* * *

Jack leaned back in his chair and watched the others in the group on the balcony, his main interest was Ianto, he wasn't the same man he'd said goodbye to a year ago, the young Welshman had grown, he wasn't the bitter man who'd greeted him in the video link back when he'd first tracked him to the SGC or the lost, lonely man with a haunted air about him that Jack had known in Cardiff. The job on the Daedalus and the love of Lindsey Novak had changed Ianto beyond all recognition, Jack could see the confidence that he'd never seen in Ianto before, the way he laughed and joked with the Atlantis crew that had joined in this particular party, even the way he reacted to the Doctor. Jack had made a point of introducing them, Ianto had been a little stiff at first but after they had talked for a while he could see Ianto unbending, maybe even understanding what the Doctor had gone through at the battle of Canary Wharf, he couldn't quite suppress the little spark of jealousy when he saw the way Ianto looked at Lindsey, he'd never looked at him that way, open and honest joy of love and being loved in return, he could see why Ianto had done everything he could to get Lisa back, he would do the same for Lindsey too. Jack watched Myfanwy showing off, diving for fish and making Delilah's stepdaughter laugh, he watched Tosh, Radek and the Doctor arguing over some scientific problem and Donna telling a joke to Delilah and her husband Evan, Ianto and Lindsey were standing at the rail watching the sunset, Jack sighed as he wandered over to join the group, everyone was happy, especially him, he could travel the stars again with a clear conscious. 


End file.
